Figure 1

Schematic overview of RNA sequencing data analysis. A total of eight datasets were processed by aligning the 50-bp paired-end sequencing reads to the human transcriptome, the M. bovis BCG genome, and/or the M. bovis BCG gene and small RNA sequences. Six of these datasets were used for differential gene and/or small RNA expression analysis. (THP: Reference dataset for the THP-1 transcriptome, EGB: Reference dataset for the (exponentially growing) M. bovis BCG transcriptome, SPI: Spike-in dataset, IF0/1/2: Datasets of M. bovis BCG bacilli infecting THP-1 cells, IF1/2ER: Datasets of M. bovis BCG cells infecting THP-1 cells enriched for M. bovis BCG bacilli).